Mobile Suit Gundam SEED: Seeds of Shadows
by ShadowCell
Summary: AU rewrite, prologue to other stories. The year is CE 71 and war is coming to an end at the cataclysmic Second Battle of Jachin Due, but one fateful choice leads a handful of soldiers down a dark and terrible path.


Mobile Suit Gundam SEED - Seeds of Shadows

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Disclaimer: _Mobile Suit Gundam SEED_ is the property of Bandai and Sunrise, not me. I make no money off this little venture. This is purely for entertainment purposes, and no copyright infringement is intended.

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I think _Gundam SEED_ and, more specifically and severely, _Gundam SEED DESTINY_ suck. I have made this known to people. Some of _DESTINY_'s most ardent fans have, in their own way, challenged me to do better.

So I will.

In order to facilitate the changes I intend to make to _DESTINY_, I need to make some changes to the ending of _Gundam SEED_, which is what I'm doing here. This little prologue will explain most the future changes I intend to make to _DESTINY_. It also serves as an alternate ending to _SEED_. This needs to be read first in order to figure out the changes in the _DESTINY_ rewrite. The subsequent fanfics are "The Power to Protect" (which focuses on Kira); "Pain" (which focuses on Clotho Buer, Orga Sabnak, and Shani Andras); "Soldiers of Old" (which focuses on a whole set of characters, primarily Athrun and Cagalli); "Golden Goddess" (which likewise focuses on Athrun and Cagalli); and "Mobile Suit Gundam SEED DESTINY" (which focuses on all sorts of people, but primarily revolves around Shinn Asuka and Stella Loussier).

I will post a new chapter every Friday, or the soonest day thereafter should something arise on Friday to keep me from posting.

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**September 27th, CE 71 - Near ZAFT space fortress Jachin Due, Lagrange Point 5**

It was called Jachin Due. This giant asteroid, peppered with metallic constructs, was the sole surviving space fortress of ZAFT. A fleet was arrayed before it, a massive armada of blue and green, curved, almost alien-looking warships; and before that fleet was another fleet, its ships more conventionally-shaped and colored in nondescript grays, distinctly the enemy's. There was a battle going on. Flashes of green beam fire and missiles and machinegun fire filled the black sky. Explosions tore apart space. People died.

The beam shots flashed by as Athrun Zala's Justice Gundam, nestled within the menacing confines of its METEOR support system, roared towards Jachin Due. Atop the Justice's subflight lifter crouched Cagalli Yula Athha's Strike Rouge, and to Athrun's left was Kira Yamato's Freedom Gundam, also protected in a METEOR.

Somewhere behind him, Athrun heard the duel between the _Archangel_ and the _Dominion_ draw to a close. An Earth Alliance Strike Dagger charged towards the _Archangel_, but Mwu La Fllaga's Aile Strike Gundam took it down with a beam shot. The _Dominion_'s three Gundams closed in, in defense of their mothership, but the _Archangel_'s Lohengrin cannons fired and slammed into the _Dominion_'s bridge. A moment later the ship exploded into a multi-armed fireball, ripping the ship's center apart and sending the engines and legs flying, and the Strike backed away as the _Dominion_'s three now-orphaned mobile suits floated around the wreck, motionless.

There was no time to reflect—all that remained now to Athrun Zala was the fortress ahead, and the massive superweapon GENESIS that hung in space next to it. It had to be stopped—not just GENESIS, but this entire war, before anymore blood was needlessly shed. He had to break in on foot, find the main command center, find his father, and stop him and his weapon and his war before they all went out of control.

"Kira," Cagalli's voice crackled over the radio. "Are you alright?"

Kira was silent.

"Kira?" Athrun asked.

"...yes," Kira answered at last. Athrun gazed inquisitively at his friend. Something was wrong.

A pair of GINNs stormed towards them, and Athrun cut off his rumination to blast off their heads with his METEOR's beam cannons.

Kira had gone through some kind of hardship, but wasn't letting on what. Athrun cleared it from his mind and returned his focus to the fortress; soon it would all be over, and they could return to their peaceful lives. Kira would be okay. Cagalli would be okay. Lacus would be okay. It would all be okay, as long as he could get to that fortress and stop this war.

Kira's METEOR broke off and disappeared in another direction.

"Kira!" Cagalli shouted. Athrun looked over at Kira in confusion. _Where is he_—?

"Something's come up," he said shortly. "Look after Cagalli."

Athrun looked on ahead, and magnified the scene, to find Rau Le Creuset's Providence Gundam, its DRAGOON units weaving a web of beam shots around the Buster Gundam. There was the _Dominion_'s escape ship not far away. Athrun momentarily thought of breaking off to help, but Kira was on his way there. He would deal with it.

"Understood," he said quietly.

The METEOR roared on towards the fortress.

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The beam shots slashed through the Buster Gundam's Phase Shift armor, and as the cockpit machinery threw sparks and warning lights flashed, Dearka Elthman cursed. The Providence's DRAGOON units darted around him, surrounding him in beam fire. In a series of hits, the Buster's left arm, head, and right leg were gone, and the Buster's power was almost fully depleted. He cursed and looked back up at the victorious Providence.

"Dearka!"

Dearka blinked and looked up, finding Yzak Jule's Duel Gundam Assault Shroud diving in to the rescue. Beam shots from the Providence forced it away; then a storm of missiles flashed around the hulking Providence, and Kira's Freedom Gundam dropped in with a slash from its METEOR beam saber. The Providence and its DRAGOON units moved off to engage the Freedom, and Yzak's Duel moved towards the ruined Buster.

"Dearka! Can you move?!" Yzak exclaimed, as the Duel took hold of the Buster's remaining arm.

Dearka tried to move the Buster's controls, but nothing happened. "No," he answered. "There was a power surge. The battery is fried."

"Shit," Yzak muttered. The Duel glanced around the battlefield. A Strike Dagger came shrieking in, firing its beam rifle, but Yzak protected the wounded Buster with the Duel's shield and fired back, taking down the attacker in two shots to the torso.

Dearka looked over at the Duel. Yzak was bound by ZAFT military law to capture him and return him to his ZAFT superiors, where he would surely face execution. He had deserted and fought against his own side and killed ZAFT soldiers. He knew he had done the right thing, but his ZAFT superiors would not see things his way. He closed his eyes, expecting the end.

"The legged ship," Yzak said unexpectedly. "I'll take you back there. Where is it?"

Dearka blinked in surprise. _Archangel_? Would Yzak take him there? But he would be punished too.

"Yzak, ZAFT will come after you too if you do that!" he yelled. "I'm going to go back to ZAFT in chains to die, I can accept that, now don't go down with me!"

"Not if there's anything I can do about it!" Yzak snapped back. "Now tell me where the goddamn legged ship is!"

"I'm serious, Yzak, you'll be indicted too!" Dearka exclaimed. "I did what I did, I don't regret it, now the end's here and I just have to face it! Stop trying to go down with me!"

"Like hell I will!" Yzak shouted. Dearka fell silent, blinking again. "You did what you did, I did what I did, there's nothing either of us can do about it now, but I'm sure as hell not going to leave you out here! Now for the last fucking time, tell me where the legged ship is!"

Dearka looked away. Yzak didn't care about the consequences; he never did. Dearka resignedly punched in the coordinates, and Yzak's Duel took off towards the _Archangel_.

"You won't get a warm welcome," Dearka warned.

"Whatever," Yzak grunted.

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"You again, eh?"

The Providence Gundam's DRAGOON units flashed around the Freedom, showering it with beam fire. Kira tried to charge through the net, but a volley of shots blocked his path. He looked up and saw the Providence, and heard the voice of Rau Le Creuset.

"You shouldn't even exist!" Rau snarled. Kira ignited one of the METEOR's beam sabers and took a swipe, but the Providence expertly dodged and dove in with its own saber to slash the METEOR's saber in half. Kira abandoned the ruined weapon as it exploded and charged on with his remaining saber ignited. "If anyone discovered you," Rau went on, as the Providence dodged again and surrounded the Freedom with beam shots, "they'd want to be like your _kind_..."

The Providence's DRAGOON units flashed in, forcing Kira back, and the Providence itself sliced the second beam saber in half as well. Kira drew the Freedom's sabers and hurriedly deflected the Providence's shots, boxed in by the DRAGOON units.

"You know," Rau laughed as the Providence descended on the helpless Freedom. "You're not a person! You're not even a Coordinator! You're just an experiment, a tool, a weapon!"

The Freedom dodged as a beam shot slashed near its head. "I'm not just a weapon!" Kira exclaimed, firing back with the Freedom's cannons.

The Providence dove out of the way. "And who will understand that?!" Rau laughed. The Providence's DRAGOON units darted around Kira again, as he backpedaled away from the Providence itself. "No one will understand!" he shouted. The DRAGOON units stormed in, Kira found his METEOR being blasted away from the Freedom, and the Providence itself raged in for the kill. "_No matter who!_"

The Providence came down with a beam saber slash, and Kira ejected the remaining parts of the METEOR before they exploded around him. He drew the Freedom's shield and beam rifle and went on the attack. Rau laughed as Kira charged.

"It's useless!" he cackled as the Freedom struggled to hit him and was surrounded in a web of beam fire. "You know you're fighting for the wrong thing!" Rau looked off to the side, as the DRAGOON units fenced Kira in. The _Dominion_'s escape shuttle was there—and there she was, Fllay Allster, another piece to this puzzle. He flashed a grin towards the Freedom, feeling a twinge of pressure from his white-armored foe— Kira had detected Fllay's presence, although he would not yet know how or why…and if Rau had his way, he never would.

The Freedom slithered out of the net the DRAGOON units had woven and charged, and Rau deflected the Freedom's beam saber swing with the Providence's shield. The mobile suits parted again, and the Freedom dove through an opening in the DRAGOON volleys.

"You know as well as I do that if you go back you'll be just a weapon!" Rau cried.

"You don't know anything!" Kira shouted, as the Freedom stormed forward with its saber. The mobile suits met again in a shower of sparks.

"Of course I don't know!" Rau cackled. "Humans only know what they think they know!"

The Providence shoulder-rammed the Freedom and knocked it away, forcing it back on the defensive. Kira grunted in frustration, charging back into the Providence's face.

"'One day,'" Rau laughed, as the beam sabers clashed again, "'one day they'll understand!'" He pushed the Freedom away and bombarded it with beam shots again. "That's what you said! Well they _don't_ understand! And they never will!"

Kira grunted in pain as the Freedom rattled. "You're wrong!" he shouted.

"Am I?!" Rau laughed again, as the DRAGOON units went on the attack again. "Eyes that see only blood, hearts that feel only hatred, hands that know only how to pull a trigger, and you say I'm wrong?" The Providence came down with a slash, and the Freedom repelled the saber stroke with its shield. With a beam shot, the two mobile suits separated again. Rau fired his beam rifle back at the Freedom, nearly clipping its leg. The mobile suits clashed again in a beam saber lock. "Look at that thing, GENESIS! Does it look like something made by creatures that _won't_ destroy themselves?!"

"You're wrong!" Kira cried.

Rau laughed maniacally. "We'll see who's wrong, little Kira!"

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**ZAFT space fortress Jachin Due**

Here it was: the main command center. It had taken several tense gunfights with ZAFT guards, but Athrun, Cagalli, and an M1 Astray pilot accompanying them both had managed to fight their way in.

The door opened with a hiss, and Athrun tensed. This was the main command center. His father would be in here. The controls to GENESIS would be in here. The means to stop this war would be in here. He just had to get inside.

He glanced into the room and prepared to dive in, but he stopped short. There was blood—

His father was there, dead, surrounded in floating globs of blood. Another dead ZAFT officer drifted away from him. The room's remaining occupants were in shock, staring at the two dead bodies.

"What happened…?" Cagalli murmured. Athrun's eyes widened in horror at his father's bleeding corpse.

"F-Father!" he exclaimed, rushing forward towards his father's body. The remaining ZAFT officers looked up at him, and some, recognizing his face, raised weapons and opened fire. From the doorway, Cagalli and their M1 pilot escort returned fire, forcing the ZAFT officers back, as Athrun drifted to his father's corpse. "Father! Father, speak to me!"

Patrick Zala said nothing. Athrun lowered his head, grinding his teeth against his tears.

"Athrun!" Cagalli exclaimed. "Athrun, we have to do something about GENESIS!"

"Princess, get up there," the M1 pilot instructed gruffly, forcing the ZAFT officers back with machinegun fire. Cagalli dove up to Athrun's side as the pilot covered her, and she grabbed Athrun by the shoulders. "Athrun, I know you're upset but we have to move _now_! There's no time!"

Athrun looked at her with dull eyes.

"We have to stop this thing now, before anyone else ends up like him!" she cried, gesturing to Patrick's dead body. "You'll know what to do in here!"

Athrun looked up at the computer terminal controlling GENESIS, and blinked at the sound of gunshots. Cagalli took up her gun and returned fire, diving to the rescue of their pilot companion.

"I'll cover you!" Cagalli shouted. "Just stop this thing!"

Athrun moved to the terminal and began typing furiously, struggling to put his father's death out of his mind and focus.

"I'll remove the safeties on the reactor," he murmured to himself, hoping to forget his father for now, "and start a reaction that should take it down."

"Whatever you're doing, hurry!" Cagalli shouted above the gunshots. "We can't hold them off forever!"

"Princess," the M1 pilot grunted, "Rocky reports trouble at our MS."

"Shit," Cagalli growled. "Athrun, hurry!"

Athrun furrowed his brow and set to work. "Give me a minute," he answered. "I'm taking off the reactor's safeties and starting a reaction to superheat the reactor. This will take it out."

He smacked the final key and then raised his machinegun, blasting out the terminal with a volley of shots. "Let's go!" he shouted.

As Cagalli and the M1 pilot made their escape, Athrun paused to glance at Patrick's body. His eyes clouded with tears as he turned and escaped.

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**Near ZAFT space fortress Jachin Due**

"You've gotta be kidding me," Mwu grunted, looking at the screen of the Strike Gundam. He floated over the _Archangel_'s right leg, as the Duel Gundam brought in the damaged Buster. A GINN came rushing in to stop them, but Mwu took it down with a single shot. He returned his attention to the screen. "_Archangel!_ Look at this!"

There was a pause. Murrue Ramius gasped in surprise. "GENESIS's heat levels are rising!" she exclaimed.

"It'll blow at this rate," Mwu said, looking back at the Coordinator superweapon. "Where are Athrun and Cagalli?!"

Murrue looked away. "They...went to take it out," she said quietly. Mwu's eyes widened.

"What?!" he cried. "Are they—"

There was a flash of beam fire, and Mwu threw the Strike's shield to defense. A Strike Dagger came flying in, but the Duel Gundam was there to take it down with a beam shot. Mwu glanced in surprise at the Duel.

"Don't worry about him," Dearka's static-broken voice put in, as the Buster stumbled into the _Archangel_'s hangar.

Mwu looked back out at GENESIS.

"But...where's Kira?"

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Rau paused, glancing down at his screen. GENESIS's heat signature was rising—soon it would be destroyed. Someone must have tampered with the reactor to—

He pushed the thoughts out of his mind and swarmed his DRAGOON units around the Freedom Gundam again. It didn't matter if GENESIS was destroyed now. He glanced pointedly back at the _Dominion_'s escape shuttle, and smirked. He had an even better weapon now.

"Kira!"

Rau's smirk grew feral as he saw the Justice Gundam, accompanied by the Strike Rouge and two M1 Astrays, come darting into the fray. The final piece had arrived.

The Justice opened fire with its beam rifle, and Rau dodged, splitting a handful of DRAGOON units off to deal with Athrun. The Providence ignited its beam saber and dropped in to slam it against the Justice's shield.

"You too, Athrun?!" Rau laughed. The Freedom swung in to help, but the DRAGOON units rose to meet him.

"Athrun!" Kira cried as the Freedom was forced back. Rau looked over at the shuttle and pulled away, pulling his DRAGOON units back to encompass the battlefield. He darted towards the shuttle, positioned himself in front of it, and fired at the Justice. Athrun grunted as the shot slammed against his shield, and raised his own beam rifle to attack.

Rau grinned, and time slowed to a crawl.

Kira watched the Justice fire, but the shot missed the Providence. He opened his mouth to scream, but no sound came out. The shot drilled through the _Dominion_'s escape shuttle—

"FLLAY!"

Athrun's beam rifle fell, the DRAGOON units went silent, and the Providence backed away.

"K-Kira," Athrun stuttered, "I—"

Kira cut him off with a sob, staring in horror, tears clouding his eyes, at the field of debris that remained of the _Dominion_'s escape shuttle.

"Fllay!" he screamed, the Freedom diving down towards the debris. "Fllay! You can't—Fllay! FLLAY!"

The Freedom stopped amidst the debris, as Athrun watched in horror and Rau in amusement.

"Kira!" Athrun exclaimed. "I was aiming at Rau, but—"

"YOU KILLED HER!" Kira shrieked. The Freedom turned and roared up towards the Justice to slam its saber against Athrun's shield. Athrun grunted under the blow. "YOU KILLED HER, ATHRUN!"

"Kira!" Athrun exclaimed. "You don't understand, Kira! I didn't—"

"YOU KILLED HER!"

The Freedom pressed its attack, firing its railguns and plasma cannons as it tore down towards the Justice. Athrun dove out of the way of the attack and deflected the follow-up saber strike, diving away from the Freedom.

The Providence retrieved its DRAGOON units and quietly slipped away.

"YOU KILLED HER!" Kira screamed as the Freedom charged. "ATHRUN! YOU KILLED HER! YOU—"

Then the world went white.

Athrun's instinct kicked in and he dove behind a warship wreck, as GENESIS began its fiery death throes. Risking one last glance around the battlefield, he latched onto the wreck to ride out the blast.

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**Earth Alliance _Agamemnon_-class carrier _John Adams_**

Pain.

That was the only thing registering in the mind of Shani Andras. He was vaguely aware that he was lying on a bed, but how he got here, why, when it was, what had happened, where the Forbidden Gundam was, where _he_ was...everything was blurred out by the pain.

"Well, I don't feel right just leaving them like this," a voice said. Shani vaguely remembered him being someone important— an officer, perhaps. He remembered having been in space before this, so perhaps he was aboard a battleship. The middle-aged man in the Earth Alliance uniform looked pityingly at him as he writhed on the bed. Somewhere behind him, Clotho Buer screamed out in pain, and Orga Sabnak was gripping his chest and on the verge of screaming himself.

"I know," another person agreed, maybe the doctor or something, Shani didn't know. "But they were on Gamma Glipheptin, and they're going through withdrawal right now."

"Can't we give them a small enough dose to ease the pain or something?" the captain asked. The doctor shook his head, dismayed.

"The only ship in the fleet that had any of that was the _Dominion_."

The captain nodded in understanding. "And the _Dominion_ was destroyed...I understand." He looked away angrily. "Goddamn Azrael...'biological CPU' indeed." He looked back at the doctor. "But still, can't you give them morphine or something?"

The doctor looked back at Shani skeptically. "I'm not sure what would happen," he said dubiously. "I don't know the nature of Gamma Glipheptin well enough to predict the effects, but I don't think Director Azrael wanted painkillers to be able to lessen the effect of the withdrawal. It might kill them."

The captain looked away angrily. "Dammit," he grumbled. "Well, I suppose all we can do is let them ride this out, if giving them painkillers is too dangerous." He turned away. "I'll be on the bridge. Try to keep them stable."

The doctor saluted. "Yes sir. I'll report back to you when they've calmed down a bit."

The captain left the room, and Shani lost himself in the pain.

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**Three Ships Alliance battleship _Archangel_, en route to Lagrange Point 3**

"I understand."

Murrue looked away shamefully. She had envisioned the end of the war as something joyous, but this was hardly a joyful occasion. Athrun stood before her on the bridge of the _Archangel_, his face sad.

"I couldn't find Kira after the blast," he said sullenly. "I have to assume..." He trailed off, not willing to finish.

In the bridge controls, Milly and Sai looked down somberly.

Athrun glanced across the bridge. Yzak Jule was leaning there, arms crossed, staring neutrally at him.

"We can't go back to Orb," Murrue said quietly. "The Seirans have taken over there, and they're extremely unfriendly to Athha family supporters like us." She looked out the bridge windows. "And Kira's gone."

"What will we do?" Athrun asked. Murrue looked back at him.

"Cagalli wants to fight the Seirans," she answered. "We're going to Heliopolis to refit ourselves into something that can actually take them on. There's bound to be something useful left over there, and no one would think to look there anyways, even if Artemis is nearby. Besides, we still have some friends in the Junk Guild." She shrugged her shoulders. "We're basically going to be space pirates. That's how it sounded when she described it to me, anyways."

Athrun looked over at Yzak. "And, what about Yzak?"

Yzak looked away indignantly. "He can't go back to ZAFT," Milly explained softly. "Not after helping Dearka get back here."

"Besides, PLANT's new leadership will be looking to try him for war crimes," Sai added. "If you ask me, he's safer with us."

Yzak grunted in acknowledgement. Athrun figured that Milly and Sai were right.

"You're welcome to leave if you like, Athrun," Murrue said. "You too, Mr. Jule. I won't like it, and Cagalli certainly won't, but if you don't want to fight a civil war against the Orb government, then that's your business."

Athrun sighed and looked out the bridge windows.

"No," he answered. "I'll stay." He glanced over at Yzak. "You don't have a problem with staying with us, Yzak?"

Yzak shook his head, still looking indifferent.

Athrun sighed once more and looked back at Murrue.

"We'll need you to help secure Heliopolis when we get there," she said. "Mwu is in the war room right now with Andy, planning it all out, but we still need some people to make sure nobody's left any traps." She paused. "Cagalli is on the _Kusanagi_ and has requested to see you."

Athrun reluctantly straightened up and saluted. "I understand," he said. "I'll be on my way then."

He closed his eyes for a moment, shutting out the pain, and turned and left the bridge. Murrue sank into her chair and sighed.

The _Archangel_ silently glided into space.

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**Near ZAFT space fortress Jachin Due**

It was over. Finally over. GENESIS was a field of radioactive debris. Both sides were too exhausted and shattered to fight. There was nothing left but peace.

Inside the Providence, Rau smirked and glanced at the Freedom Gundam, charred and pitted and blackened but still whole, as it aimlessly drifted in space. He moved towards it and found Kira still alive, quietly weeping. The time was right—soon he would have a weapon even more powerful than GENESIS. And he knew just how to finish this little puzzle.

"Fllay," Kira murmured mournfully, as the Freedom drifted. "Fllay...why..."

"Kira," Rau spoke, gently, paternally. Kira opened his tear-brimmed eyes and recoiled in horror at the approaching Providence. "Kira, come with me."

Kira blinked. "Come...with you?"

"You want Fllay back," he said calmly. "Come with me. I can return her to you."

"But she's..." He trailed off and sobbed again.

"Kira, stay with me," Rau said soothingly. "Be calm, Kira. I can return her to you. Trust me."

Kira looked back at Rau with cloudy eyes.

"Come with me, Kira," Rau went on. "You and I are the same. I know what you're experiencing. Your friends have betrayed you, Kira. I will not." The Providence extended its hand.

Kira hesitated, staring at the outstretched mobile suit hand.

"I will give you what Lacus could not," Rau said. "I will give you the power to protect your world."

Kira stared at the Providence's hand for a moment, and then took it.

Rau smiled. The Providence and the Freedom rocketed away.

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To be continued...


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